X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandoptionparser.cpp;h=e356afe5c74972e5298ddfa87a0672c97c4facfe;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=e4db11d1993f3ee257b36b010fb22944abc3b1cd;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index e4db11d..e356afe 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -8,7 +8,6 @@
  */
 
 
-#include "globaldata.hpp"
 #include "commandoptionparser.hpp"
 
 
@@ -16,6 +15,8 @@
 //This Function parses through the command line and pulls out the command then sends the options to  the parseGlobalData
 CommandOptionParser::CommandOptionParser(string input){
 	try {
+		m = MothurOut::getInstance();
+		
 		int openParen = input.find_first_of('(');
 		int closeParen = input.find_last_of(')');
 		optionString = "";
@@ -25,21 +26,16 @@ CommandOptionParser::CommandOptionParser(string input){
 			commandString = input.substr(0, openParen);   //commandString contains everything before "("
 			optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
 		}
-		else if (openParen == -1) { cout << "You are missing (" << endl; }
-		else if (closeParen == -1) { cout << "You are missing )" << endl; }
+		else if (openParen == -1) { m->mothurOut("[ERROR]: You are missing ("); m->mothurOutEndLine(); }
+		else if (closeParen == -1) { m->mothurOut("[ERROR]:You are missing )"); m->mothurOutEndLine(); }
 					
 		//GlobalData* globaldata = GlobalData::getInstance();
 		//globaldata->parseGlobalData(commandString, optionString);			//parser to separate and check options
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the CommandOptionParser class Function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "CommandOptionParser", "CommandOptionParser");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the CommandOptionParser class function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 //**********************************************************************************************************************